transcript_archetypes: transcript_archetypes
In CshlSiepelLab/nascentRNASim:

Contructs an object that holds the transcript archetypes models

transcript_archetypes(
  transcripts,
  bigwig_plus,
  bigwig_minus,
  flank = 5000,
  abundance_filter = 100,
  mask = c(1000, 1000),
  abundance_err_func = c("identity")
)

`transcripts`	a GRanges-class object containing a pre-filtered list of transcripts that show a clear signal that arises from only that transcript with negligible signal from other sources
`bigwig_plus`	polymerase density signal from the plus strand
`bigwig_minus`	polymerase density signal from the minus strand
`flank`	the length of the flanking region for which data is collected for use in simulation
`abundance_filter`	minimal abundance value for a viable archetype gene, all transcripts with an estimated abundance less than this are removed (default = 100)
`mask`	a two element vector containing the number of bases to ignore at the head and tail of the transcript when estimating abundance
`abundance_err_func`	Error function to use when estimating abundance (defaults to identity)